I would have to do a /clearfocus at the beginning of the macro, right?
Basically, yes. If you use /focus in your main macro (to follow, etc.) and/or in your targeting macros then you'll need to clearfocus in the polymorph macro. You're also correct that hitting the main macro (again, to follow, etc.) before your new focus is dead could reset focus (depends on the use of clearfocus and some other possibilities in your setup).

Here's an example

I personally don't use a /focus based multiboxing setup. I run PVE teams so I'm content with using the standard /target party1 & /assit party1 type macro setups. If my tank goes down I'm high-tailing it out or wiping. This allows me to use /focus exclusively for crowd control. Now, that's not to say that you cannot use /focus based setups and still succesfully use /focus for CC...it simply didn't suit my macro & play styles.

Edit: I should actually clarify my first paragraph above. You can actually set your /focus in a separate macro from the /cast polymorph macro. Thus, your /clearfocus statement would belong with whatever macro is used to set /focus on a target.